int Sequence::scoreDegeneracy()
{
cout << "Score Degeneracy" << name << seqLen << endl;
int f = 0;
if (degenComputed == false)
{
char _2foldTest = '*';
char _4foldTest = '*';
int aaseqLen = seqLen/3;
int i = 0;
for (i; i < aaseqLen; i++)
{
_4foldTest = is4FoldDegenerateSite(i);
_2foldTest = is2FoldDegenerateSite(i,_4foldTest);
degScores.totalCodons++
if (_2foldTest != '*')
{
degScores.totalCodons_2fold++;
if (_2foldTest == 'A')
{
degScores.total_2fold_A++;
}
else if (_2foldTest == 'T')
{
degScores.total_2fold_T++;
}
else if (_2foldTest == 'G')
{
degScores.total_2fold_G++;
}
else
{
degScores.total_2fold_C++;
}
}else if (_4foldTest != '*')
{
degScores.totalCodons_4fold++;
if (_4foldTest == 'A')
{
degScores.total_4fold_A++;
}
else if (_4foldTest == 'T')
{
degScores.total_4fold_T++;
}
else if (_4foldTest == 'C')
{
degScores.total_4fold_C++;
}
else
{
degScores.total_4fold_G++;
}
}
cout << "Crashes right here when i = 0." << endl;
}
}
degenComputed = true;
return 1;
}
让我疯了！ SegFault恰好在for循环的第一次迭代结束时发生。行为完全像它应该的那样，首先测试返回正确的结果..分段错误发生在我甚至递增之前....
我错过了什么？
...
char Sequence::is4FoldDegenerateSite(int codonIndex){
char aminoAcid = aaSeq[codonIndex];
//cout << "Amino acid of codon number " << codonIndex << " is: " << aminoAcid << endl;
int loc = readingFrame + (codonIndex * 3) + 2;
int locR = loc - 2;
switch (aminoAcid){
case 'A':
return seq[loc];
case 'T':
return seq[loc];
case 'V':
return seq[loc];
case 'G':
return seq[loc];
case 'P':
return seq[loc];
case 'S'://Can also be 2 fold degenerate
if (seq[locR] == 'T'){
return seq[loc];
}else{
return '*';
}
case 'R'://Can also be 2 fold degenerate
if (seq[locR] == 'C'){
return seq[loc];
}else{
return '*';
}
case 'L'://Can also be 2 fold degenerate
if (seq[locR] == 'C'){
return seq[loc];
}else{
return '*';
}
}
return '*';
}
char Sequence::is2FoldDegenerateSite(int codonIndex, char _4FoldResults){
char aminoAcid = aaSeq[codonIndex];
int loc = readingFrame + (codonIndex * 3) + 2;
//char doubleDegeneracyTest = is4FoldDegenerateSite(codonIndex);
//bool doubleDegeneracy = false;
//if (doubleDegeneracyTest != '*') doubleDegeneracy = true;
switch (aminoAcid){
case 'N':
return seq[loc];
case 'D':
return seq[loc];
case 'C':
return seq[loc];
case 'Q':
return seq[loc];
case 'E':
return seq[loc];
case 'H':
return seq[loc];
case 'K':
return seq[loc];
case 'F':
return seq[loc];
case 'Y':
return seq[loc];
case 'X':
return seq[loc];
case 'S'://Can also be 2 fold degenerate
if (_4FoldResults == '*'){
return seq[loc];
}else{
return '*';
}
case 'R'://Can also be 2 fold degenerate
if (_4FoldResults == '*'){
return seq[loc];
}else{
return '*';
}
case 'L'://Can also be 2 fold degenerate
if (_4FoldResults == '*'){
return seq[loc];
}else{
return '*';
}
}
return '*';
}
Valgrind结果：
**17043** new/new[] failed and should throw an exception, but Valgrind
==17043== at 0x4024E35: VALGRIND_PRINTF_BACKTRACE (valgrind.h:3720)
==17043== by 0x40253C2: operator new(unsigned int) (vg_replace_malloc.c:214)
==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D70A7: std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D7EDC: std::string::reserve(unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D83AF: std::string::append(std::string const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x804BA7F: std::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (basic_string.h:2168)
==17043== by 0x804ACDF: GenomeSeq::setup() (GenomeSeq.C:108)
==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52)
==17043== by 0x80496DF: main (Main2.C:143)
**17043** cannot throw exceptions and so is aborting instead. Sorry.
==17043== at 0x4024E35: VALGRIND_PRINTF_BACKTRACE (valgrind.h:3720)
==17043== by 0x40253D0: operator new(unsigned int) (vg_replace_malloc.c:214)
==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D70A7: std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D7EDC: std::string::reserve(unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D83AF: std::string::append(std::string const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x804BA7F: std::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (basic_string.h:2168)
==17043== by 0x804ACDF: GenomeSeq::setup() (GenomeSeq.C:108)
==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52)
==17043== by 0x80496DF: main (Main2.C:143)
Loading sequence..==17043==
==17043== HEAP SUMMARY:
==17043== in use at exit: 2,749,679 bytes in 10 blocks
==17043== total heap usage: 39,043 allocs, 39,032 frees, 80,022,672,644 bytes allocated
==17043==
==17043== 27 bytes in 1 blocks are definitely lost in loss record 1 of 10
==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214)
==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D7340: ??? (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D7525: std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x804969E: main (Main2.C:143)
==17043==
==17043== 28 bytes in 1 blocks are definitely lost in loss record 2 of 10
==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214)
==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D7340: ??? (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D7525: std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x80496C3: main (Main2.C:143)
==17043==
==17043== 83 bytes in 1 blocks are definitely lost in loss record 3 of 10
==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214)
==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D70A7: std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D7EDC: std::string::reserve(unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D814A: std::string::append(char const*, unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40B3F3E: std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, char) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40C9799: std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x804ACB5: GenomeSeq::setup() (GenomeSeq.C:106)
==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52)
==17043== by 0x80496DF: main (Main2.C:143)
==17043==
==17043== 100 bytes in 1 blocks are definitely lost in loss record 4 of 10
==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214)
==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D70A7: std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D7EDC: std::string::reserve(unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D814A: std::string::append(char const*, unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40B3F3E: std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&, char) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40C9799: std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x804AC07: GenomeSeq::setup() (GenomeSeq.C:101)
==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52)
==17043== by 0x80496DF: main (Main2.C:143)
==17043==
==17043== 100 bytes in 1 blocks are definitely lost in loss record 5 of 10
==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214)
==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D7340: ??? (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D75D1: std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D33C5: std::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >::basic_istringstream(std::string const&, std::_Ios_Openmode) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x804AC42: GenomeSeq::setup() (GenomeSeq.C:103)
==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52)
==17043== by 0x80496DF: main (Main2.C:143)
==17043==
==17043== 8,192 bytes in 1 blocks are definitely lost in loss record 8 of 10
==17043== at 0x4025024: operator new[](unsigned int) (vg_replace_malloc.c:258)
==17043== by 0x40A2592: std::basic_filebuf<char, std::char_traits<char> >::_M_allocate_internal_buffer() (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40A65B1: std::basic_filebuf<char, std::char_traits<char> >::open(char const*, std::_Ios_Openmode) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40A7EAF: std::basic_ifstream<char, std::char_traits<char> >::basic_ifstream(char const*, std::_Ios_Openmode) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x804ABBF: GenomeSeq::setup() (GenomeSeq.C:97)
==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52)
==17043== by 0x80496DF: main (Main2.C:143)
==17043==
==17043== 8,192 bytes in 1 blocks are definitely lost in loss record 9 of 10
==17043== at 0x4025024: operator new[](unsigned int) (vg_replace_malloc.c:258)
==17043== by 0x40A2592: std::basic_filebuf<char, std::char_traits<char> >::_M_allocate_internal_buffer() (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40A65B1: std::basic_filebuf<char, std::char_traits<char> >::open(char const*, std::_Ios_Openmode) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40A7EAF: std::basic_ifstream<char, std::char_traits<char> >::basic_ifstream(char const*, std::_Ios_Openmode) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x804AC9D: GenomeSeq::setup() (GenomeSeq.C:105)
==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52)
==17043== by 0x80496DF: main (Main2.C:143)
==17043==
==17043== 2,732,253 bytes in 1 blocks are definitely lost in loss record 10 of 10
==17043== at 0x4025390: operator new(unsigned int) (vg_replace_malloc.c:214)
==17043== by 0x40D6435: std::string::_Rep::_S_create(unsigned int, unsigned int, std::allocator<char> const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D70A7: std::string::_Rep::_M_clone(std::allocator<char> const&, unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D7EDC: std::string::reserve(unsigned int) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x40D83AF: std::string::append(std::string const&) (in /usr/lib/libstdc++.so.6.0.13)
==17043== by 0x804BA7F: std::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) (basic_string.h:2168)
==17043== by 0x804ACDF: GenomeSeq::setup() (GenomeSeq.C:108)
==17043== by 0x804A4FE: GenomeSeq::GenomeSeq(std::string, std::string) (GenomeSeq.C:52)
==17043== by 0x80496DF: main (Main2.C:143)
==17043==
==17043== LEAK SUMMARY:
==17043== definitely lost: 2,748,975 bytes in 8 blocks
==17043== indirectly lost: 0 bytes in 0 blocks
==17043== possibly lost: 0 bytes in 0 blocks
==17043== still reachable: 704 bytes in 2 blocks
==17043== suppressed: 0 bytes in 0 blocks
==17043== Reachable blocks (those to which a pointer was found) are not shown.
==17043== To see them, rerun with: --leak-check=full --show-reachable=yes
==17043==
==17043== For counts of detected and suppressed errors, rerun with: -v
==17043== ERROR SUMMARY: 8 errors from 8 contexts (suppressed: 19 from 8)
Sequence.h：
#ifndef SEQUENCE_H
#define SEQUENCE_H
using namespace std;
#include <iostream>
#include <fstream>
#include <cstring>
#include <sstream>
#include <string>
class GeneSeqs;
class Sequence{
public:
Sequence();
Sequence(char * seqStart,char * aaSeqStart, int length);//Constructor
~Sequence();//Destructor -- for the transprof
//void setup();//Setups up variables.
char &operator[](int);
char * getSeq(){return seq;}//returns the address of sequence
string getAASeq(){return aaSeq;}//returns address of aaSeq
int getLength(){return seqLen;}
bool isPositive(){return positiveStrand;}
/**
* Setters
*/
void setRevC(char * sequ){revC = sequ;}
void setSeq(char * sequ){
seq = sequ;
}
void setAASeq(char * a){aaSeq = a;}
void setLength(int len){seqLen = len;}
void setAALength(int len){aaSeqLen = len;}
void setPositivity(bool trufal){
positiveStrand = trufal;
if (trufal == false){
buildRevC();
}
}
//
int getTCount(){return count.T;}
int getACount(){return count.A;}
int getCCount(){return count.C;}
int getGCount(){return count.G;}
//void setAASeq(int * a){aaSeq = a;}
string get_aaSeq(){return aaSeq;}
bool get_aaSeqExhists(){return aaSeqTranslated;}
int get_aaSeqLen(){return aaSeqLen;}
void print();
void printAA();
char getAA(int i){return aaSeq[i];}
int getAALoc(char aa){return AAchar2num(aa);}
float getMIMScore(){return MIMScore;}
void setMIM(float MIM){MIMScore = MIM;}
void translateToAA(int code);
void computeCrudeCompositions();
int scoreDegeneracy();
void degeneracyReport();
void setName(string n){name = n;}
float distanceMeasure(Sequence * target);
bool degeneracyIsScored(){return degenComputed;}
float distanceMeasure(GeneSeqs * target);
float distanceMeasureA(GeneSeqs * target, int point, float runningSum);
int getDegenData(int code);
void setStartConstant(int i){start = i;}
void printInfo();
private:
struct nucleotideCounts{
int T;
int C;
int A;
int G;
}count;
struct degeneracyScores{
int totalCodons;
int totalCodons_4fold;
int totalCodons_2fold;
int total_4fold_A;
int total_4fold_T;
int total_4fold_C;
int total_4fold_G;
int total_2fold_A;
int total_2fold_T;
int total_2fold_G;
int total_2fold_C;
}degScores;
string name;
char is4FoldDegenerateSite(int codonIndex);
char is2FoldDegenerateSite(int codonIndex, char _4FoldResults);
bool degenComputed;
float MIMScore;
void buildRevC();
string revC;
char nucleoRevC(char c);
char * seq;
int readingFrame;//zero till used...
int aaSeqLen;
bool aaSeqTranslated;
int start;
int seqLen; //Number of nucleotides in sequence
bool positiveStrand; //Positive strand = true, negative = false;
//bool hasY;
//Genetic sequence in numerical Amino Acide representation;
string aaSeq;
void geneSegments2AASeq();
void computeAATransProf();
int AAchar2num(char x);
char AAnum2char(int x);
char codon2AA(int codonIndex);
char codon2AA(char * codon);
char codon2AA(int * codon);
int Int(string num);
int Int(char num);
char num2nucleo(int a);
void codonSeq2AASeq();
int char2nucleo2(char a);
string String(int num);
};
#endif
答案 0 :(得分：5)
total heap usage: 39,043 allocs, 39,032 frees, 80,022,672,644 bytes allocated
80GB ??我觉得你某处有内存泄漏......
我会投票给你处理“seq”作为char *的方式，而不是在其他地方使用std：string。看起来像是一场等待发生的事故。
答案 1 :(得分：4)
你是在unix还是linux机器上？如果是这样，Valgrind是解决这类问题的绝佳工具。
答案 2 :(得分：4)
is4FoldDegenerateSite或is2FoldDegenerateSite正在破坏您的堆栈，然后当程序尝试分支回到for的开头时，堆栈关闭，因此您分支到坏内存。
查看这两个功能并确保它们正确清理内存。你有可以发布的那些功能的代码吗？
编辑：
您重载了[]运算符。也许这是个好看的地方？陌生人远程调试代码非常复杂。
答案 3 :(得分：1)
开始逐件删除（阻止评论很有帮助）以找出影响崩溃的因素。正确性与此故障排除技术无关。如果删除任何东西修复它，你可能正在寻找系统性的东西。
可悲的事实是，您的问题不是崩溃站点的本地问题，因此在崩溃站点周围发送碎片并不足以让我们发现您的错误。
答案 4 :(得分：1)
我严重怀疑你在Sequence类中处理seq变量的方式。 现在，我建议你添加
bool Sequence::isValid (int loc){
if ((seq != NULL) && (loc < strlen(seq))) { return true; } // optimize it later
else { return false; }
}
并更新is4FoldDegenerateSite（）＆amp;＆amp; is2FoldDegenerateSite（）包含以下内容，
int loc = readingFrame + (codonIndex * 3) + 2;
int locR = loc - 2;
if (isValid(loc) == false) return '*';
// also validate locR before using it.
在我看来，你还应该添加一些异常处理;更新setSeq（char * sequ）＆amp; setLength（int len）在输入无效的情况下抛出异常。
HTH